diff --git a/src/skill_seekers/cli/doc_scraper.py b/src/skill_seekers/cli/doc_scraper.py
index 74b1ee0..1e52181 100755
--- a/src/skill_seekers/cli/doc_scraper.py
+++ b/src/skill_seekers/cli/doc_scraper.py
@@ -349,6 +349,151 @@ class DocToSkillConverter:
 
         return page
 
+    def _extract_markdown_content(self, content: str, url: str) -> Dict[str, Any]:
+        """Extract content from a Markdown file.
+
+        Args:
+            content: Raw markdown content (or HTML if server returned HTML)
+            url: Source URL
+
+        Returns:
+            Page dict with title, content, code_samples, headings, links
+        """
+        import re
+
+        # Detect if content is actually HTML (some .md URLs return HTML)
+        if content.strip().startswith('<!DOCTYPE') or content.strip().startswith('<html'):
+            return self._extract_html_as_markdown(content, url)
+
+        page = {
+            'url': url,
+            'title': '',
+            'content': '',
+            'headings': [],
+            'code_samples': [],
+            'patterns': [],
+            'links': []
+        }
+
+        lines = content.split('\n')
+
+        # Extract title from first h1
+        for line in lines:
+            if line.startswith('# '):
+                page['title'] = line[2:].strip()
+                break
+
+        # Extract headings (h2-h6)
+        for line in lines:
+            match = re.match(r'^(#{2,6})\s+(.+)$', line)
+            if match:
+                level = len(match.group(1))
+                text = match.group(2).strip()
+                page['headings'].append({
+                    'level': f'h{level}',
+                    'text': text,
+                    'id': text.lower().replace(' ', '-')
+                })
+
+        # Extract code blocks with language
+        code_blocks = re.findall(r'```(\w+)?\n(.*?)```', content, re.DOTALL)
+        for lang, code in code_blocks:
+            if len(code.strip()) > 10:
+                page['code_samples'].append({
+                    'code': code.strip(),
+                    'language': lang or 'unknown'
+                })
+
+        # Extract content (paragraphs)
+        content_no_code = re.sub(r'```.*?```', '', content, flags=re.DOTALL)
+        paragraphs = []
+        for para in content_no_code.split('\n\n'):
+            text = para.strip()
+            # Skip headings and short text
+            if text and len(text) > 20 and not text.startswith('#'):
+                paragraphs.append(text)
+        page['content'] = '\n\n'.join(paragraphs)
+
+        # Extract links from markdown (only .md files to avoid client-side rendered HTML pages)
+        md_links = re.findall(r'\[([^\]]*)\]\(([^)]+)\)', content)
+        for _, href in md_links:
+            if href.startswith('http'):
+                full_url = href
+            elif not href.startswith('#'):
+                full_url = urljoin(url, href)
+            else:
+                continue
+            # Strip anchor fragments
+            full_url = full_url.split('#')[0]
+            # Only include .md URLs to avoid client-side rendered HTML pages
+            if '.md' in full_url and self.is_valid_url(full_url) and full_url not in page['links']:
+                page['links'].append(full_url)
+
+        return page
+
+    def _extract_html_as_markdown(self, html_content: str, url: str) -> Dict[str, Any]:
+        """Extract content from HTML and convert to markdown-like structure.
+
+        Args:
+            html_content: Raw HTML content
+            url: Source URL
+
+        Returns:
+            Page dict with title, content, code_samples, headings, links
+        """
+        page = {
+            'url': url,
+            'title': '',
+            'content': '',
+            'headings': [],
+            'code_samples': [],
+            'patterns': [],
+            'links': []
+        }
+
+        soup = BeautifulSoup(html_content, 'html.parser')
+
+        # Try to extract title
+        title_elem = soup.select_one('title')
+        if title_elem:
+            page['title'] = self.clean_text(title_elem.get_text())
+
+        # Try to find main content area
+        main = soup.select_one('main, article, [role="main"], .content')
+        if not main:
+            main = soup.body if soup.body else soup
+
+        if main:
+            # Extract headings
+            for h in main.find_all(['h1', 'h2', 'h3', 'h4', 'h5', 'h6']):
+                text = self.clean_text(h.get_text())
+                if text:
+                    page['headings'].append({
+                        'level': h.name,
+                        'text': text,
+                        'id': h.get('id', '')
+                    })
+
+            # Extract code blocks
+            for code_elem in main.select('pre code, pre'):
+                code = code_elem.get_text()
+                if len(code.strip()) > 10:
+                    lang = self.detect_language(code_elem, code)
+                    page['code_samples'].append({
+                        'code': code.strip(),
+                        'language': lang
+                    })
+
+            # Extract paragraphs
+            paragraphs = []
+            for p in main.find_all('p'):
+                text = self.clean_text(p.get_text())
+                if text and len(text) > 20:
+                    paragraphs.append(text)
+            page['content'] = '\n\n'.join(paragraphs)
+
+        return page
+
     def detect_language(self, elem, code):
         """Detect programming language from code block
 
@@ -386,14 +531,19 @@ class DocToSkillConverter:
         return text.strip()
     
     def save_page(self, page: Dict[str, Any]) -> None:
-        """Save page data"""
+        """Save page data (skip pages with empty content)"""
+        # Skip pages with empty or very short content
+        if not page.get('content') or len(page.get('content', '')) < 50:
+            logger.debug("Skipping page with empty/short content: %s", page.get('url', 'unknown'))
+            return
+
         url_hash = hashlib.md5(page['url'].encode()).hexdigest()[:10]
         safe_title = re.sub(r'[^\w\s-]', '', page['title'])[:50]
         safe_title = re.sub(r'[-\s]+', '_', safe_title)
-        
+
         filename = f"{safe_title}_{url_hash}.json"
         filepath = os.path.join(self.data_dir, "pages", filename)
-        
+
         with open(filepath, 'w', encoding='utf-8') as f:
             json.dump(page, f, indent=2, ensure_ascii=False)
     
@@ -408,6 +558,7 @@ class DocToSkillConverter:
 
         Note:
             Uses threading locks when workers > 1 for thread safety
+            Supports both HTML pages and Markdown (.md) files
         """
         try:
             # Scraping part (no lock needed - independent)
@@ -415,8 +566,12 @@ class DocToSkillConverter:
             response = requests.get(url, headers=headers, timeout=30)
             response.raise_for_status()
 
-            soup = BeautifulSoup(response.content, 'html.parser')
-            page = self.extract_content(soup, url)
+            # Check if this is a Markdown file
+            if url.endswith('.md') or '.md' in url:
+                page = self._extract_markdown_content(response.text, url)
+            else:
+                soup = BeautifulSoup(response.content, 'html.parser')
+                page = self.extract_content(soup, url)
 
             # Thread-safe operations (lock required)
             if self.workers > 1:
@@ -463,6 +618,7 @@ class DocToSkillConverter:
 
         Note:
             Uses asyncio.Lock for async-safe operations instead of threading.Lock
+            Supports both HTML pages and Markdown (.md) files
         """
         async with semaphore:  # Limit concurrent requests
             try:
@@ -471,9 +627,13 @@ class DocToSkillConverter:
                 response = await client.get(url, headers=headers, timeout=30.0)
                 response.raise_for_status()
 
-                # BeautifulSoup parsing (still synchronous, but fast)
-                soup = BeautifulSoup(response.content, 'html.parser')
-                page = self.extract_content(soup, url)
+                # Check if this is a Markdown file
+                if url.endswith('.md') or '.md' in url:
+                    page = self._extract_markdown_content(response.text, url)
+                else:
+                    # BeautifulSoup parsing (still synchronous, but fast)
+                    soup = BeautifulSoup(response.content, 'html.parser')
+                    page = self.extract_content(soup, url)
 
                 # Async-safe operations (no lock needed - single event loop)
                 logger.info("  %s", url)
@@ -493,6 +653,56 @@ class DocToSkillConverter:
             except Exception as e:
                 logger.error("  ✗ Error scraping %s: %s: %s", url, type(e).__name__, e)
 
+    def _convert_to_md_urls(self, urls: List[str]) -> List[str]:
+        """
+        Convert URLs to .md format, trying /index.html.md suffix for non-.md URLs.
+        不预先检查 URL 是否存在，直接加入队列，在爬取时再验证。
+
+        Args:
+            urls: List of URLs to process
+
+        Returns:
+            List of .md URLs (未验证)
+        """
+        md_urls = []
+
+        for url in urls:
+            if '.md' in url:
+                md_urls.append(url)
+            else:
+                # 直接转换为 .md 格式，不发送 HEAD 请求检查
+                url = url.rstrip('/')
+                md_url = f"{url}/index.html.md"
+                md_urls.append(md_url)
+
+        logger.info("  ✓ Converted %d URLs to .md format (will validate during crawl)", len(md_urls))
+        return md_urls
+
+    # ORIGINAL _convert_to_md_urls (with HEAD request validation):
+    # def _convert_to_md_urls(self, urls: List[str]) -> List[str]:
+    #     md_urls = []
+    #     non_md_urls = []
+    #     for url in urls:
+    #         if '.md' in url:
+    #             md_urls.append(url)
+    #         else:
+    #             non_md_urls.append(url)
+    #     if non_md_urls:
+    #         logger.info("  🔄 Trying to convert %d non-.md URLs to .md format...", len(non_md_urls))
+    #         converted = 0
+    #         for url in non_md_urls:
+    #             url = url.rstrip('/')
+    #             md_url = f"{url}/index.html.md"
+    #             try:
+    #                 resp = requests.head(md_url, timeout=5, allow_redirects=True)
+    #                 if resp.status_code == 200:
+    #                     md_urls.append(md_url)
+    #                     converted += 1
+    #             except Exception:
+    #                 pass
+    #         logger.info("  ✓ Converted %d URLs to .md format", converted)
+    #     return md_urls
+
     def _try_llms_txt(self) -> bool:
         """
         Try to use llms.txt instead of HTML scraping.
@@ -548,7 +758,29 @@ class DocToSkillConverter:
                             logger.info("     ✓ %s (%d chars)", extra_filename, len(extra_content))
 
                 # Parse explicit file for skill building
-                parser = LlmsTxtParser(content)
+                parser = LlmsTxtParser(content, self.base_url)
+
+                # Extract URLs from llms.txt and add to pending_urls for BFS crawling
+                extracted_urls = parser.extract_urls()
+                if extracted_urls:
+                    # Convert non-.md URLs to .md format by trying /index.html.md suffix
+                    md_urls = self._convert_to_md_urls(extracted_urls)
+                    logger.info("\n🔗 Found %d URLs in llms.txt (%d .md files), starting BFS crawl...",
+                               len(extracted_urls), len(md_urls))
+
+                    # Filter URLs based on url_patterns config
+                    for url in md_urls:
+                        if self.is_valid_url(url) and url not in self.visited_urls:
+                            self.pending_urls.append(url)
+
+                    logger.info("  📋 %d URLs added to crawl queue after filtering", len(self.pending_urls))
+
+                    # Return False to trigger HTML scraping with the populated pending_urls
+                    self.llms_txt_detected = True
+                    self.llms_txt_variant = 'explicit'
+                    return False  # Continue with BFS crawling
+
+                # Fallback: if no URLs found, use section-based parsing
                 pages = parser.parse()
 
                 if pages:
@@ -606,7 +838,29 @@ class DocToSkillConverter:
         largest = max(downloaded.items(), key=lambda x: x[1]['size'])
         logger.info("\n📄 Parsing %s for skill building...", largest[1]['filename'])
 
-        parser = LlmsTxtParser(largest[1]['content'])
+        parser = LlmsTxtParser(largest[1]['content'], self.base_url)
+
+        # Extract URLs from llms.txt and add to pending_urls for BFS crawling
+        extracted_urls = parser.extract_urls()
+        if extracted_urls:
+            # Convert non-.md URLs to .md format by trying /index.html.md suffix
+            md_urls = self._convert_to_md_urls(extracted_urls)
+            logger.info("\n🔗 Found %d URLs in llms.txt (%d .md files), starting BFS crawl...",
+                       len(extracted_urls), len(md_urls))
+
+            # Filter URLs based on url_patterns config
+            for url in md_urls:
+                if self.is_valid_url(url) and url not in self.visited_urls:
+                    self.pending_urls.append(url)
+
+            logger.info("  📋 %d URLs added to crawl queue after filtering", len(self.pending_urls))
+
+            # Return False to trigger HTML scraping with the populated pending_urls
+            self.llms_txt_detected = True
+            self.llms_txt_variants = list(downloaded.keys())
+            return False  # Continue with BFS crawling
+
+        # Fallback: if no URLs found, use section-based parsing
         pages = parser.parse()
 
         if not pages:
diff --git a/src/skill_seekers/cli/llms_txt_parser.py b/src/skill_seekers/cli/llms_txt_parser.py
index e288c92..2e143bf 100644
--- a/src/skill_seekers/cli/llms_txt_parser.py
+++ b/src/skill_seekers/cli/llms_txt_parser.py
@@ -3,12 +3,67 @@
 
 import re
 from typing import List, Dict
+from urllib.parse import urljoin
 
 class LlmsTxtParser:
     """Parse llms.txt markdown content into page structures"""
 
-    def __init__(self, content: str):
+    def __init__(self, content: str, base_url: str = None):
         self.content = content
+        self.base_url = base_url
+
+    def extract_urls(self) -> List[str]:
+        """
+        Extract all URLs from the llms.txt content.
+
+        Returns:
+            List of unique URLs found in the content
+        """
+        urls = set()
+
+        # Match markdown links: [text](url)
+        md_links = re.findall(r'\[([^\]]*)\]\(([^)]+)\)', self.content)
+        for _, url in md_links:
+            if url.startswith('http'):
+                clean_url = self._clean_url(url)
+                if clean_url:
+                    urls.add(clean_url)
+            elif self.base_url and not url.startswith('#'):
+                clean_url = self._clean_url(urljoin(self.base_url, url))
+                if clean_url:
+                    urls.add(clean_url)
+
+        # Match bare URLs
+        bare_urls = re.findall(r'https?://[^\s\)\]<>"\']+', self.content)
+        for url in bare_urls:
+            # Clean trailing punctuation
+            url = url.rstrip('.,;:')
+            clean_url = self._clean_url(url)
+            if clean_url:
+                urls.add(clean_url)
+
+        return list(urls)
+
+    def _clean_url(self, url: str) -> str:
+        """
+        Clean and validate URL, removing invalid anchor patterns.
+
+        Args:
+            url: URL to clean
+
+        Returns:
+            Cleaned URL or empty string if invalid
+        """
+        # Skip URLs with path after anchor (e.g., #section/index.html.md)
+        # These are malformed and return duplicate HTML content
+        if '#' in url:
+            anchor_pos = url.index('#')
+            after_anchor = url[anchor_pos + 1:]
+            # If there's a path separator after anchor, it's invalid
+            if '/' in after_anchor:
+                # Extract the base URL without the malformed anchor
+                return url[:anchor_pos]
+        return url
 
     def parse(self) -> List[Dict]:
         """
diff --git a/src/skill_seekers/cli/unified_scraper.py b/src/skill_seekers/cli/unified_scraper.py
index f8b5dcf..f294f89 100644
--- a/src/skill_seekers/cli/unified_scraper.py
+++ b/src/skill_seekers/cli/unified_scraper.py
@@ -70,8 +70,12 @@ class UnifiedScraper:
         self.merge_mode = merge_mode or self.config.get('merge_mode', 'rule-based')
         logger.info(f"Merge mode: {self.merge_mode}")
 
-        # Storage for scraped data
-        self.scraped_data = {}
+        # Storage for scraped data - use lists to support multiple sources of same type
+        self.scraped_data = {
+            'documentation': [],  # List of doc sources
+            'github': [],         # List of github sources
+            'pdf': []             # List of pdf sources
+        }
 
         # Output paths
         self.name = self.config['name']
@@ -81,6 +85,9 @@ class UnifiedScraper:
         os.makedirs(self.output_dir, exist_ok=True)
         os.makedirs(self.data_dir, exist_ok=True)
 
+        # Track source index for unique naming
+        self._source_counters = {'documentation': 0, 'github': 0, 'pdf': 0}
+
     def scrape_all_sources(self):
         """
         Scrape all configured sources.
@@ -114,13 +121,22 @@ class UnifiedScraper:
                 logger.error(f"Error scraping {source_type}: {e}")
                 logger.info("Continuing with other sources...")
 
-        logger.info(f"\n✅ Scraped {len(self.scraped_data)} sources successfully")
+        logger.info(f"\n✅ Scraped {sum(len(v) for v in self.scraped_data.values())} sources successfully")
 
     def _scrape_documentation(self, source: Dict[str, Any]):
         """Scrape documentation website."""
-        # Create temporary config for doc scraper
+        # Get unique index for this documentation source
+        idx = self._source_counters['documentation']
+        self._source_counters['documentation'] += 1
+
+        # Extract source identifier from URL for unique naming
+        from urllib.parse import urlparse
+        parsed = urlparse(source['base_url'])
+        source_id = parsed.netloc.replace('.', '_').replace(':', '_')
+
+        # Create temporary config for doc scraper with unique name
         doc_config = {
-            'name': f"{self.name}_docs",
+            'name': f"{self.name}_docs_{idx}_{source_id}",
             'base_url': source['base_url'],
             'selectors': source.get('selectors', {}),
             'url_patterns': source.get('url_patterns', {}),
@@ -164,10 +180,15 @@ class UnifiedScraper:
             with open(docs_data_file, 'r', encoding='utf-8') as f:
                 summary = json.load(f)
 
-            self.scraped_data['documentation'] = {
+            # Append to list instead of overwriting
+            self.scraped_data['documentation'].append({
+                'source_id': source_id,
+                'base_url': source['base_url'],
                 'pages': summary.get('pages', []),
-                'data_file': docs_data_file
-            }
+                'total_pages': summary.get('total_pages', 0),
+                'data_file': docs_data_file,
+                'refs_dir': f"output/{doc_config['name']}/references"
+            })
 
             logger.info(f"✅ Documentation: {summary.get('total_pages', 0)} pages scraped")
         else:
@@ -185,10 +206,18 @@ class UnifiedScraper:
             logger.error("github_scraper.py not found")
             return
 
+        # Get unique index for this GitHub source
+        idx = self._source_counters['github']
+        self._source_counters['github'] += 1
+
+        # Extract repo identifier for unique naming
+        repo = source['repo']
+        repo_id = repo.replace('/', '_')
+
         # Create config for GitHub scraper
         github_config = {
-            'repo': source['repo'],
-            'name': f"{self.name}_github",
+            'repo': repo,
+            'name': f"{self.name}_github_{idx}_{repo_id}",
             'github_token': source.get('github_token'),
             'include_issues': source.get('include_issues', True),
             'max_issues': source.get('max_issues', 100),
@@ -197,7 +226,7 @@ class UnifiedScraper:
             'include_code': source.get('include_code', True),
             'code_analysis_depth': source.get('code_analysis_depth', 'surface'),
             'file_patterns': source.get('file_patterns', []),
-            'local_repo_path': source.get('local_repo_path')  # Pass local_repo_path from config
+            'local_repo_path': source.get('local_repo_path')
         }
 
         # Pass directory exclusions if specified (optional)
@@ -207,19 +236,22 @@ class UnifiedScraper:
             github_config['exclude_dirs_additional'] = source['exclude_dirs_additional']
 
         # Scrape
-        logger.info(f"Scraping GitHub repository: {source['repo']}")
+        logger.info(f"Scraping GitHub repository: {repo}")
         scraper = GitHubScraper(github_config)
         github_data = scraper.scrape()
 
-        # Save data
-        github_data_file = os.path.join(self.data_dir, 'github_data.json')
+        # Save data with unique filename
+        github_data_file = os.path.join(self.data_dir, f'github_data_{idx}_{repo_id}.json')
         with open(github_data_file, 'w', encoding='utf-8') as f:
             json.dump(github_data, f, indent=2, ensure_ascii=False)
 
-        self.scraped_data['github'] = {
+        # Append to list instead of overwriting
+        self.scraped_data['github'].append({
+            'repo': repo,
+            'repo_id': repo_id,
             'data': github_data,
             'data_file': github_data_file
-        }
+        })
 
         logger.info(f"✅ GitHub: Repository scraped successfully")
 
@@ -274,14 +306,23 @@ class UnifiedScraper:
             logger.info("No API merge needed (only one API source)")
             return []
 
-        # Get documentation and GitHub data
-        docs_data = self.scraped_data.get('documentation', {})
-        github_data = self.scraped_data.get('github', {})
+        # Get documentation and GitHub data (now lists)
+        docs_list = self.scraped_data.get('documentation', [])
+        github_list = self.scraped_data.get('github', [])
 
-        if not docs_data or not github_data:
+        if not docs_list or not github_list:
             logger.warning("Missing documentation or GitHub data for conflict detection")
             return []
 
+        # For conflict detection, combine all docs and all github data
+        # Use the first of each for now (conflict detection is optional)
+        docs_data = docs_list[0] if docs_list else {}
+        github_data = github_list[0] if github_list else {}
+
+        if not docs_data.get('data_file') or not github_data.get('data_file'):
+            logger.warning("Missing data files for conflict detection")
+            return []
+
         # Load data files
         with open(docs_data['data_file'], 'r', encoding='utf-8') as f:
             docs_json = json.load(f)
@@ -328,9 +369,17 @@ class UnifiedScraper:
             logger.info("No conflicts to merge")
             return None
 
-        # Get data files
-        docs_data = self.scraped_data.get('documentation', {})
-        github_data = self.scraped_data.get('github', {})
+        # Get data files (now lists)
+        docs_list = self.scraped_data.get('documentation', [])
+        github_list = self.scraped_data.get('github', [])
+
+        if not docs_list or not github_list:
+            logger.warning("Missing data for merge")
+            return None
+
+        # Use first source of each type for merge
+        docs_data = docs_list[0]
+        github_data = github_list[0]
 
         # Load data
         with open(docs_data['data_file'], 'r', encoding='utf-8') as f:
diff --git a/src/skill_seekers/cli/unified_skill_builder.py b/src/skill_seekers/cli/unified_skill_builder.py
index b8f9700..a80f86d 100644
--- a/src/skill_seekers/cli/unified_skill_builder.py
+++ b/src/skill_seekers/cli/unified_skill_builder.py
@@ -268,118 +268,177 @@ This skill combines knowledge from multiple sources:
         """Generate reference files organized by source."""
         logger.info("Generating reference files...")
 
-        # Generate references for each source type
-        if 'documentation' in self.scraped_data:
-            self._generate_docs_references()
+        # Generate references for each source type (now lists)
+        docs_list = self.scraped_data.get('documentation', [])
+        if docs_list:
+            self._generate_docs_references(docs_list)
 
-        if 'github' in self.scraped_data:
-            self._generate_github_references()
+        github_list = self.scraped_data.get('github', [])
+        if github_list:
+            self._generate_github_references(github_list)
 
-        if 'pdf' in self.scraped_data:
-            self._generate_pdf_references()
+        pdf_list = self.scraped_data.get('pdf', [])
+        if pdf_list:
+            self._generate_pdf_references(pdf_list)
 
         # Generate merged API reference if available
         if self.merged_data:
             self._generate_merged_api_reference()
 
-    def _generate_docs_references(self):
-        """Generate references from documentation source."""
+    def _generate_docs_references(self, docs_list: List[Dict]):
+        """Generate references from multiple documentation sources."""
         docs_dir = os.path.join(self.skill_dir, 'references', 'documentation')
         os.makedirs(docs_dir, exist_ok=True)
 
-        # Best-effort: copy docs-only reference files into unified docs references.
-        # UnifiedScraper runs doc_scraper using name "{name}_docs", which creates
-        # output/{name}_docs/references/*.md. Those are the most useful documentation
-        # references for the unified skill.
-        source_refs_dir = os.path.join('output', f"{self.name}_docs", 'references')
-        copied_files: List[str] = []
+        all_copied_files: List[str] = []
 
-        if os.path.isdir(source_refs_dir):
-            for entry in sorted(os.listdir(source_refs_dir)):
-                src_path = os.path.join(source_refs_dir, entry)
-                dst_path = os.path.join(docs_dir, entry)
-                if not os.path.isfile(src_path):
-                    continue
-                shutil.copy2(src_path, dst_path)
-                copied_files.append(entry)
+        # Process each documentation source
+        for i, doc_source in enumerate(docs_list):
+            source_id = doc_source.get('source_id', f'source_{i}')
+            base_url = doc_source.get('base_url', 'Unknown')
+            refs_dir = doc_source.get('refs_dir', '')
 
-        # Create index
+            # Create subdirectory for this source
+            source_dir = os.path.join(docs_dir, source_id)
+            os.makedirs(source_dir, exist_ok=True)
+
+            copied_files: List[str] = []
+
+            if refs_dir and os.path.isdir(refs_dir):
+                for entry in sorted(os.listdir(refs_dir)):
+                    src_path = os.path.join(refs_dir, entry)
+                    dst_path = os.path.join(source_dir, entry)
+                    if not os.path.isfile(src_path):
+                        continue
+                    shutil.copy2(src_path, dst_path)
+                    copied_files.append(entry)
+
+            # Create index for this source
+            source_index_path = os.path.join(source_dir, 'index.md')
+            with open(source_index_path, 'w', encoding='utf-8') as f:
+                f.write(f"# Documentation: {source_id}\n\n")
+                f.write(f"**Source**: {base_url}\n\n")
+                f.write(f"**Pages**: {doc_source.get('total_pages', 'N/A')}\n\n")
+
+                if copied_files:
+                    files_no_index = [p for p in copied_files if p.lower() != 'index.md']
+                    f.write("## Files\n\n")
+                    for filename in files_no_index:
+                        f.write(f"- [{filename}]({filename})\n")
+                else:
+                    f.write("No reference files available.\n")
+
+            all_copied_files.extend(copied_files)
+
+        # Create main index
         index_path = os.path.join(docs_dir, 'index.md')
         with open(index_path, 'w', encoding='utf-8') as f:
-            f.write("# Documentation\n\n")
-            f.write("Reference from official documentation.\n\n")
+            f.write("# Documentation References\n\n")
+            f.write(f"Combined from {len(docs_list)} documentation sources.\n\n")
 
-            if copied_files:
-                files_no_index = [p for p in copied_files if p.lower() != 'index.md']
-                files_index = [p for p in copied_files if p.lower() == 'index.md']
+            f.write("## Sources\n\n")
+            for doc_source in docs_list:
+                source_id = doc_source.get('source_id', 'unknown')
+                base_url = doc_source.get('base_url', 'Unknown')
+                total_pages = doc_source.get('total_pages', 'N/A')
+                f.write(f"- [{source_id}]({source_id}/index.md) - {base_url} ({total_pages} pages)\n")
 
-                f.write("## Files\n\n")
-                for filename in files_no_index + files_index:
-                    f.write(f"- [{filename}]({filename})\n")
-            else:
-                f.write("## Notes\n\n")
-                f.write(
-                    "No documentation reference files were copied into this unified skill. "
-                    "This usually means the docs-only build did not produce reference files.\n"
-                )
+        logger.info(f"Created documentation references ({len(docs_list)} sources)")
 
-        logger.info("Created documentation references")
-
-    def _generate_github_references(self):
-        """Generate references from GitHub source."""
+    def _generate_github_references(self, github_list: List[Dict]):
+        """Generate references from multiple GitHub sources."""
         github_dir = os.path.join(self.skill_dir, 'references', 'github')
         os.makedirs(github_dir, exist_ok=True)
 
-        github_data = self.scraped_data['github']['data']
+        # Process each GitHub source
+        for i, github_source in enumerate(github_list):
+            repo = github_source.get('repo', f'repo_{i}')
+            repo_id = github_source.get('repo_id', repo.replace('/', '_'))
+            github_data = github_source.get('data', {})
 
-        # Create README reference
-        if github_data.get('readme'):
-            readme_path = os.path.join(github_dir, 'README.md')
-            with open(readme_path, 'w') as f:
-                f.write("# Repository README\n\n")
-                f.write(github_data['readme'])
+            # Create subdirectory for this repo
+            repo_dir = os.path.join(github_dir, repo_id)
+            os.makedirs(repo_dir, exist_ok=True)
 
-        # Create issues reference
-        if github_data.get('issues'):
-            issues_path = os.path.join(github_dir, 'issues.md')
-            with open(issues_path, 'w') as f:
-                f.write("# GitHub Issues\n\n")
-                f.write(f"{len(github_data['issues'])} recent issues.\n\n")
+            # Create README reference
+            if github_data.get('readme'):
+                readme_path = os.path.join(repo_dir, 'README.md')
+                with open(readme_path, 'w', encoding='utf-8') as f:
+                    f.write(f"# Repository README: {repo}\n\n")
+                    f.write(github_data['readme'])
 
-                for issue in github_data['issues'][:20]:
-                    f.write(f"## #{issue['number']}: {issue['title']}\n\n")
-                    f.write(f"**State**: {issue['state']}\n")
-                    if issue.get('labels'):
-                        f.write(f"**Labels**: {', '.join(issue['labels'])}\n")
-                    f.write(f"**URL**: {issue.get('url', 'N/A')}\n\n")
+            # Create issues reference
+            if github_data.get('issues'):
+                issues_path = os.path.join(repo_dir, 'issues.md')
+                with open(issues_path, 'w', encoding='utf-8') as f:
+                    f.write(f"# GitHub Issues: {repo}\n\n")
+                    f.write(f"{len(github_data['issues'])} recent issues.\n\n")
 
-        # Create releases reference
-        if github_data.get('releases'):
-            releases_path = os.path.join(github_dir, 'releases.md')
-            with open(releases_path, 'w') as f:
-                f.write("# Releases\n\n")
+                    for issue in github_data['issues'][:20]:
+                        f.write(f"## #{issue['number']}: {issue['title']}\n\n")
+                        f.write(f"**State**: {issue['state']}\n")
+                        if issue.get('labels'):
+                            f.write(f"**Labels**: {', '.join(issue['labels'])}\n")
+                        f.write(f"**URL**: {issue.get('url', 'N/A')}\n\n")
 
-                for release in github_data['releases'][:10]:
-                    f.write(f"## {release['tag_name']}: {release.get('name', 'N/A')}\n\n")
-                    f.write(f"**Published**: {release.get('published_at', 'N/A')[:10]}\n\n")
-                    if release.get('body'):
-                        f.write(release['body'][:500])
-                        f.write("\n\n")
+            # Create releases reference
+            if github_data.get('releases'):
+                releases_path = os.path.join(repo_dir, 'releases.md')
+                with open(releases_path, 'w', encoding='utf-8') as f:
+                    f.write(f"# Releases: {repo}\n\n")
 
-        logger.info("Created GitHub references")
+                    for release in github_data['releases'][:10]:
+                        f.write(f"## {release['tag_name']}: {release.get('name', 'N/A')}\n\n")
+                        f.write(f"**Published**: {release.get('published_at', 'N/A')[:10]}\n\n")
+                        if release.get('body'):
+                            f.write(release['body'][:500])
+                            f.write("\n\n")
 
-    def _generate_pdf_references(self):
-        """Generate references from PDF source."""
+            # Create index for this repo
+            repo_index_path = os.path.join(repo_dir, 'index.md')
+            repo_info = github_data.get('repo_info', {})
+            with open(repo_index_path, 'w', encoding='utf-8') as f:
+                f.write(f"# GitHub: {repo}\n\n")
+                f.write(f"**Stars**: {repo_info.get('stars', 'N/A')}\n")
+                f.write(f"**Language**: {repo_info.get('language', 'N/A')}\n")
+                f.write(f"**Issues**: {len(github_data.get('issues', []))}\n")
+                f.write(f"**Releases**: {len(github_data.get('releases', []))}\n\n")
+                f.write("## Files\n\n")
+                f.write("- [README.md](README.md)\n")
+                if github_data.get('issues'):
+                    f.write("- [issues.md](issues.md)\n")
+                if github_data.get('releases'):
+                    f.write("- [releases.md](releases.md)\n")
+
+        # Create main index
+        index_path = os.path.join(github_dir, 'index.md')
+        with open(index_path, 'w', encoding='utf-8') as f:
+            f.write("# GitHub References\n\n")
+            f.write(f"Combined from {len(github_list)} GitHub repositories.\n\n")
+
+            f.write("## Repositories\n\n")
+            for github_source in github_list:
+                repo = github_source.get('repo', 'unknown')
+                repo_id = github_source.get('repo_id', repo.replace('/', '_'))
+                github_data = github_source.get('data', {})
+                repo_info = github_data.get('repo_info', {})
+                stars = repo_info.get('stars', 'N/A')
+                f.write(f"- [{repo}]({repo_id}/index.md) - {stars} stars\n")
+
+        logger.info(f"Created GitHub references ({len(github_list)} repos)")
+
+    def _generate_pdf_references(self, pdf_list: List[Dict]):
+        """Generate references from PDF sources."""
         pdf_dir = os.path.join(self.skill_dir, 'references', 'pdf')
         os.makedirs(pdf_dir, exist_ok=True)
 
         # Create index
         index_path = os.path.join(pdf_dir, 'index.md')
-        with open(index_path, 'w') as f:
+        with open(index_path, 'w', encoding='utf-8') as f:
             f.write("# PDF Documentation\n\n")
-            f.write("Reference from PDF document.\n\n")
+            f.write(f"Reference from {len(pdf_list)} PDF document(s).\n\n")
 
-        logger.info("Created PDF references")
+        logger.info(f"Created PDF references ({len(pdf_list)} sources)")
 
     def _generate_merged_api_reference(self):
         """Generate merged API reference file."""